The Battle of Berlin began in April, 1945 and ended in May. Japan held out until September, 1945. Most people believed it would hold out much longer. General MacArthur suggested it might take ten years.
So, if there were experts who believed that Japan might hold out for another decade, why wouldn't any Nazis flee to Japan?
If Nazis had a choice of where to flee, Japan wouldn't be a very good choice because it was not safe at all in 1945. Even though the prediction for surrender may have been later, cities in Japan were already being regularly firebombed and the losses at the Battles of Iwo Jima and Okinawa presaged an Allied invasion of Japan. The military was given priority over the citizens, which cause mass starvation throughout the country. Sure, Germany and Japan had a treaty, but nowhere in WWII did they actually help each other militarily. The connections between Japan and Germany were little except for common enemies. And once Germany has surrendered, it's not like Nazis can find hope in Japan restoring Nazi Germany or something. Their war was over, so the wartime alliances were a moot point. The Japanese populace was also cultured to be ultranationalistic and anti-foreign, so it wouldn't be so friendly to Nazis coming in.